Data from: Origin of land plants revisited in the light of sequence contamination and missing data

Knowing the closest relatives of land plants is key to understanding the complex adaptations to terrestrial life. Unfortunately, multi-gene analyses yield highly incongruent results, suggesting for instance Charales, Zygnematales, or Coleochaete as the sister-group of land plants. Such controversy may result from the real history of life, in particular closely spaced speciation events, incomplete lineage sorting, gene duplication or horizontal gene transfer. In such cases, the solution resides in improved taxon sampling and sophisticated models of evolution. However, we will show that the quality of data used to infer the phylogeny may also play a major role, creating unnecessary controversy. In particular, the inclusion of contaminant sequences from other species, and of genes with incomplete taxon sampling explains a large part of the discrepancies observed between various studies. The use of a carefully checked and almost complete dataset suggests that land plants are closely related to a group composed of Zygnematales and Coleochaetales.

明确陆生植物（land plants）的最近缘类群，是理解其对陆地生活复杂适应性的核心前提。遗憾的是，多基因分析（multi-gene analyses）往往得到高度不一致的结果：不同研究曾分别将轮藻目（Charales）、接合藻目（Zygnematales）以及链藻属（Coleochaete）认定为陆生植物的姊妹群（sister-group）。这类争议或源于生命演化的真实历程：具体包括物种分化事件间隔紧密、不完全谱系分选（incomplete lineage sorting）、基因复制（gene duplication）以及水平基因转移（horizontal gene transfer）等因素。针对此类情形，常规解决方案在于优化类群取样（taxon sampling）并采用更为精细的演化模型。然而本文将证实，用于系统发育（phylogeny）推断的数据质量同样可能起到关键作用，甚至催生不必要的学术争议。具体而言，混入其他物种的污染序列（contaminant sequences）、以及类群取样不完整的基因，可解释当前不同研究间观测到的绝大多数分歧。经严格校验、覆盖度近乎完整的数据集分析结果表明：陆生植物的最近缘类群为接合藻目（Zygnematales）与链藻目（Coleochaetales）共同构成的演化支。